VSE rerendering whole video for just a simple effect
You are rendering out the timeline, so everything in the timeline is rewritten, therefore you cannot just do the new bits.

However you could render the portions with effects as seperate clips then use an external app to join them to the original. A program like ffmpeg will do this appending function, but I don't recall if you can alter the start and end time of the un-effected clip in the middle. Anyway ffmpeg is a faster tool but at this point you may as well use Blender too render it all as a single piece.